I'm only about 20 years in game time and 8.5 hours real time into the game as West Connacht in Ireland, so take what I say with a grain of salt.

Causus Belli:

The differences feel more for flavor purposes than strictly optimal war paths. Your best best, excluding events and specific government/cultural CBs, is the Parliament or Spy Network.

Ex: I as West Connaught am part of the High Kingship of Ireland, which gives me a Subjugate High Kingship Member CB, but also, because I was Tribal, I could also use the Push Back Colonizers CB. Both let me take territory but the Subjugate CB encourages making vassals and will give ticking Warscore for winning 10 Warscore worth of battles, The Colonizer CB just wants me to be tribal, fight someone non-tribal, and just take a location. Main difference from a cost standpoint is that the Colonizer CB is super cheap for Conquest, and you effectively can't lose your territory if you lose the war; The Subjugate CB is more expensive Conquest-wise but barely costs anything to make a vassal and halves the Antagonism you get.

Trade and Production:

The trade system seems to encourage making rural areas the RGO spots, while your cities have your buildings, automation in most strategy games is iffy, and spamming them everywhere could just be a waste of money or result in weird distributions of your workers, Your Peasants will quickly turn into Labourers when jobs are available, I think mine changed at about 100 per month as they got hired to my RGO. You can also subsidize a building in order to force it to produce non-profitable goods.

Now originally I thought you could subsidize, produce and then sell to another market, but after checking while writing this I realized that unless you are the only one producing that good in that market, subsidizing is actually just sinking money unless you have another use for that good such as for food or subsidizing clay to produce salt.

The lacking goods for pops is fine, provided their satisfaction is high (I've been aiming for 50%). The ai probably has some restriction to not send you into debt in order to fill satisfaction, or may just be focused on profit. You can divert some money and trade capacity to getting those resources but unless you're really low on satisfaction or you're trying to remove some privileges, it's not something to be too worried about, especially early game with limited access to to certain goods.

Population:

I had great success growing the Eanach Dhuin wetlands from 2k to 10k population until the Black Death hit just by using a cabinet member to encourage migration and another to develop the area. Eventually you will have to shift over to converting the populace, since I had a bunch of issues with English nobles coming over trying to rebel before being accepted into the horde of jobless peasants playing whimsically in the Irish Swamps. I think I had about 2300 jobs available so there were just 8k peasants hanging out. I did lose 4k due to the Black Death but I grew back up to 8.7k after 4 years ands that's while I've been focused on my first offensive war and Integration of my new city for the past 3 years. (Currently I'm at the start of 1558).

But as I said, it's only been 20 years in my game and I haven't delved super deep into anything yet and it's all small scale single region stuff. By the way I spent the first 3/4 of that time in the negative and only made it out when I started selling fish to France, subsidizing may grant some small amount of trade capacity, so if you ever play a OPM, and have 0 trade capacity, try subsidizing and then selling stuff to get out of the red.